RetrogeneDB ID:

retro_hsap_2441

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:3470663..3471652(-)
Located in intron of:ENSG00000088812
Retrocopy
information
Ensembl ID:ENSG00000230568
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SF3A3
Ensembl ID:ENSG00000183431
Aliases:SF3A3, PRP9, PRPF9, SAP61, SF3a60
Description:splicing factor 3a, subunit 3, 60kDa [Source:HGNC Symbol;Acc:10767]


Retrocopy-Parental alignment summary:






>retro_hsap_2441
ATGGAGACAATACTGGAGCAGCAGCGGCGCTATCATGAGGAGAAGGAAAGGCTCATGGACGTCATGGCCAAAGAGATGCT
CACTAAGAAGTCCACGCTCAATTCTGATCACCGCACTCAGGCCATGCAAGATAGGTATATGGAGGTCAGTGGGAACCTGA
GGGATCTGTATGATGATAAAGATGGATTATGAAAGGAGGAACTCAATGCCATTTCAGGACCCAGTGAGTTTGCTGAATTC
TATAATAGACTCGAGTAAATAAAGGAATTCCACCAGAAGCACCCAAATGAGATCTGTGTGCCAATGTCAGTGAAATTTGA
GGAGCTCCTGAAGGCTCAGAGAATCCAAGTGAAGAGGCACAAAACTTGGTGGAGTTCACAGATGAAGAGGGATATGGTCG
TTACCTCGATCTCCGTGACTGTTACCTCAAGTACATTAACGTGAAGGCATCTGAGAAGCTGGATTATATCACATACCTGT
CCATCTCTGACCAATTATTTGACATTCCTAAAGAAAGGAAGAATGCAGAGTATAAGAGATACCTAGAGATGCTGCTTGAG
TAACTTCAGGATTACACAGATAGAGTAAAGCCTCTCCAAGATCAGAATGAACTTTTTGGGAAGATTCAGGCTGAGTTTGA
GAAGAAATGGGAGAATGTGACCTTCCTGGATGGGCGAAAGAGACAAGCAGCGCTCTGACCCATGCTGGAGCCCATCTTGA
CCTCTCCGCCTTCTCCTCCTGGGAGGAGTTGGCCTCTCTGGGTTTGGACAGATTGAAATCTGCTCTCTTAGCTTTAGGCT
TGAAATGTGGCGGACCGTAGAAGAGCAAGCCCAGAGACTATTCAGTACCAAAGGAAAGTCCCTGGAGTCACTTGATAACT
CTTTGTTTGCCAAAAATCCCAAATCAAAGGGCACCAAGCGAGACATTGAGAGAACAAAGACATTGCTTTTCTAGAAGCCC
AGATCTATGAATACTCTGACTCTCAGGGA

ORF - retro_hsap_2441 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.86 %
Parental protein coverage: 66.87 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMETILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKE
METILEQQRRYHEEKERLMDVMAKEMLTKKST.....NSDHRT.AMQDRYMEVSGNLRDLYDDKDGL.KE
RetrocopyMETILEQQRRYHEEKERLMDVMAKEMLTKKST----LNSDHRTQAMQDRYMEVSGNLRDLYDDKDGL*KE
ParentalELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKAR-ENPSEEAQNLVEFTDEEGYGRY
ELNAISGP.EFAEFYNRL..IKEFH.KHPNEICVPMSV.FEELLKA..ENPSEEAQNLVEFTDEEGYGRY
RetrocopyELNAISGPSEFAEFYNRLE*IKEFHQKHPNEICVPMSVKFEELLKAQ<ENPSEEAQNLVEFTDEEGYGRY
ParentalLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNEL
LDL.DCYLKYIN.KASEKLDYITYLSI.DQLFDIPKERKNAEYKRYLEMLLE.LQDYTDRVKPLQDQNEL
RetrocopyLDLRDCYLKYINVKASEKLDYITYLSISDQLFDIPKERKNAEYKRYLEMLLE*LQDYTDRVKPLQDQNEL
ParentalFGKIQAEFEKKWENGTF-PGWPKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGG-T
FGKIQAEFEKKWEN.TF.PGW.KETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGG.T
RetrocopyFGKIQAEFEKKWENVTF<PGWAKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGG<T
ParentalLEERAQRLFSTKGKSLESLDTSLFAKNPKSKGTKRDTER-NKDIAFLEAQIYEYVEILG
.EE.AQRLFSTKGKSLESLD.SLFAKNPKSKGTKRD.ER.NKDIAFLEAQIYEY....G
RetrocopyVEEQAQRLFSTKGKSLESLDNSLFAKNPKSKGTKRDIER<NKDIAFLEAQIYEYSDSQG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .00 RPM 62 .22 RPM
bodymap2_adrenal 0 .06 RPM 79 .52 RPM
bodymap2_brain 0 .14 RPM 48 .33 RPM
bodymap2_breast 0 .04 RPM 54 .77 RPM
bodymap2_colon 0 .00 RPM 68 .16 RPM
bodymap2_heart 0 .07 RPM 22 .30 RPM
bodymap2_kidney 0 .08 RPM 60 .33 RPM
bodymap2_liver 0 .02 RPM 26 .28 RPM
bodymap2_lung 0 .00 RPM 32 .95 RPM
bodymap2_lymph_node 0 .00 RPM 48 .64 RPM
bodymap2_ovary 0 .06 RPM 116 .28 RPM
bodymap2_prostate 0 .00 RPM 66 .27 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .92 RPM
bodymap2_testis 0 .04 RPM 99 .17 RPM
bodymap2_thyroid 0 .04 RPM 80 .58 RPM
bodymap2_white_blood_cells 0 .00 RPM 87 .73 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2441 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2441 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2441 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2441 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2441 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1411
Macaca mulatta retro_mmul_631
Parental genes homology:
Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000012621 retrocopy
retro_amel_485,
Canis familiaris ENSCAFG000000032221 retrocopy
retro_cfam_176,
Callithrix jacchus ENSCJAG000000021761 retrocopy
retro_cjac_4109,
Cavia porcellus ENSCPOG000000086601 retrocopy
retro_cpor_658,
Homo sapiens ENSG00000183431 2 retrocopies
retro_hsap_2441 , retro_hsap_937,
Macropus eugenii ENSMEUG000000025343 retrocopies
retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta ENSMMUG000000231991 retrocopy
retro_mmul_631,
Monodelphis domestica ENSMODG000000177291 retrocopy
retro_mdom_269,
Nomascus leucogenys ENSNLEG000000117201 retrocopy
retro_nleu_2775,
Pan troglodytes ENSPTRG000000005592 retrocopies
retro_ptro_1411, retro_ptro_649,
Sorex araneus ENSSARG000000142041 retrocopy
retro_sara_407,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .08 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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